Difference between revisions of "CoSMo 2015"
 
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This page contains course materials for the [http://www.compneurosci.com/CoSMo/program.html CoSMo 2015] summer school.
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This page contains course materials for the [http://www.compneurosci.com/CoSMo/program.html CoSMo 2015] summer school. <br>
 
[[File:CoSMo2015_small.jpg | thumb | CoSMo logo]]
 
[[File:CoSMo2015_small.jpg | thumb | CoSMo logo]]
  
 +
----
  
 
== Introduction - overview of sensory-motor control ==
 
== Introduction - overview of sensory-motor control ==
 
''Jun 29-30'' <br>
 
''Jun 29-30'' <br>
 
Lecturers: Gunnar Blohm, Paul Schrater, Konrad Kording, John van Opstal, Pieter Medendorp <br>
 
Lecturers: Gunnar Blohm, Paul Schrater, Konrad Kording, John van Opstal, Pieter Medendorp <br>
−
 
  
 
Konrad, Weiji, Dan book
 
Konrad, Weiji, Dan book
−
[http://klab.smpp.northwestern.edu/wiki/images/8/87/Book_for_school.pdf book] <br>
+
[http://compneurosci.com/wiki/images/Book_for_school.pdf book] <br>
  
 
[[Media:SensoryMotorBlohm2015Part1.pdf | Blohm slides part 1 - computational anatomy]] <br>
 
[[Media:SensoryMotorBlohm2015Part1.pdf | Blohm slides part 1 - computational anatomy]] <br>
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[[Media:Cosmo2015PaulLec2.pdf‎  | Schrater slides part 2 - sensory-motor systems]] <br>
 
[[Media:Cosmo2015PaulLec2.pdf‎  | Schrater slides part 2 - sensory-motor systems]] <br>
 
[[Media:SensoryMotorBlohm2015Part2.pdf | Blohm slides part 2 - sensory-motor processing underlying eye movements]] <br>
 
[[Media:SensoryMotorBlohm2015Part2.pdf | Blohm slides part 2 - sensory-motor processing underlying eye movements]] <br>
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[[Media:CoSMo2015-vOpstal.pdf | van Opstal syllabus - linear systems theory]] and [[Media: Answers2Exercises-Part1.pdf | Answers Part 1]] and [[Media:  |Answers Part 2]] <br>
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[[Media:CoSMo2015-vOpstal.pdf | van Opstal syllabus - linear systems theory]] and answers to exercises [[Media: Answers2Exercises-Part1.pdf | part 1]] and [[Media:Answers-Part2.pdf | part 2]] <br>
 
[[Media:SystemsCoSMo2015-1a.pdf | van Opstal slides 1 - linear systems theory]] <br>
 
[[Media:SystemsCoSMo2015-1a.pdf | van Opstal slides 1 - linear systems theory]] <br>
 
[[Media:SystemsCoSMo2015-1b.pdf | van Opstal slides 2 - linear systems in sensory-motor control A]] <br>
 
[[Media:SystemsCoSMo2015-1b.pdf | van Opstal slides 2 - linear systems in sensory-motor control A]] <br>
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'''Afternoon tutorial 2 - Saccades (Jun 30)''' <br>
 
'''Afternoon tutorial 2 - Saccades (Jun 30)''' <br>
 
[[Media:saccademodels.zip | Saccade models (Simulink code)]] <br>
 
[[Media:saccademodels.zip | Saccade models (Simulink code)]] <br>
 +
Example of additional ways to implement a saccade model using Matlab linear systems toolbox or direct integration of the differential equations underlying the linear systems approach: [[Media:Saccade_GunnarCoSMo2015.m | Simple saccade model]] <br>
  
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----
  
  
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[[Media:HowtoModel2015.pdf | tutorial slides]] <br>
 
[[Media:HowtoModel2015.pdf | tutorial slides]] <br>
  
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----
  
  
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You can get the DREAM project from Gunnar on a USB drive.  DREAM can also be downloaded piece-wise (data sets, models, tools, and documentation) from CRCNS: http://crcns.org/data-sets/movements/dream/downloading-dream.  You will need to [https://crcns.org/join_form?came_from=http%3A//crcns.org/data-sets/movements/dream/downloading-dream create] an account on CRCNS to be able to download the project files.
 
You can get the DREAM project from Gunnar on a USB drive.  DREAM can also be downloaded piece-wise (data sets, models, tools, and documentation) from CRCNS: http://crcns.org/data-sets/movements/dream/downloading-dream.  You will need to [https://crcns.org/join_form?came_from=http%3A//crcns.org/data-sets/movements/dream/downloading-dream create] an account on CRCNS to be able to download the project files.
 
<!--[[File:AllDream.zip]]-->
 
<!--[[File:AllDream.zip]]-->
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If you want "all" of DREAM (models, tools, and documentation), click here: [http://klab.smpp.northwestern.edu/wiki/images/d/d2/AllDream.zip AllDream.zip] <br>
+
If you want "all" of DREAM (models, tools, and documentation), click here: [http://compneurosci.com/wiki/images/AllDream.zip AllDream.zip] <br>
  
 
:If you're familiar with svn and would like info/credentials for code in the repository, contact [[Ben Walker]]
 
:If you're familiar with svn and would like info/credentials for code in the repository, contact [[Ben Walker]]
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*[[Media:Wei_2010.pdf | Wei 10]] -- movement in differing force fields <br>
 
*[[Media:Wei_2010.pdf | Wei 10]] -- movement in differing force fields <br>
 
*[[Media:Young_2009.pdf | Young]] -- movement time stayed the same, but distance changed; fast, medium, slow reaches. <br>
 
*[[Media:Young_2009.pdf | Young]] -- movement time stayed the same, but distance changed; fast, medium, slow reaches. <br>
 +
 +
----
 +
 +
 +
== How to write papers ==
 +
''Jun 30 (evening)'' <br>
 +
Lecturer: Konrad Kording <br>
 +
 +
[http://compneurosci.com/wiki/images/PaperPaper_submission.pdf Paper structuring paper] <br>
 +
 +
----
 +
 +
 +
== Coding & decoding ==
 +
''Jul 1'' <br>
 +
Lecturers: Joern Diedrichsen, Nikolaus Kriegeskorte <br>
 +
 +
Please read the following papers BEFORE the tutorial: [[Media:Ejaz_NN_2015.pdf  | Ejaz, et al., 2015]] and [[Media:Kriegeskorte.pdf  | Khaligh-Razavi & Kriegeskorte, 2014]] <br>
 +
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[[Media:Kriegeskorte_cosmo_school_nijmegen_1july2015.pdf  | Niko's slides]] <br>
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[[Media:Lecture_RSA_basicJornCoSMo2015.pdf  | Joern's slides - Part 1]] <br>
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[[Media:Lecture_component_modelsJornCoSMo2015.pdf  | Joern's slides - Part 2]] <br>
 +
 +
If you would like to apply these methods, please refer to this [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003553 paper]. The link to the Matlab code can be found within the paper. Accompanying tutorial videos can be found [http://www.mrc-cbu.cam.ac.uk/rsa2015/rsa2015media/ here].
 +
 +
----
 +
 +
 +
== Motor learning & control ==
 +
''Jul 2'' <br>
 +
Lecturers: Stefan Glasauer, John van Opstal <br>
 +
 +
[[Media:Cosmo2015Glasauer.pdf | Stefan's lectures]] <br>
 +
[[Media:ControlCoSMo2015.zip | Accompanying code]] <br>
 +
 +
----
 +
 +
 +
== Multisensory processing ==
 +
''Jul 3-4'' <br>
 +
Lecturers: Kathy Cullen, Bart Krekelberg <br>
 +
 +
[[Media:2015_Linear_computational_lecture_compressed.pdf | Kathy's linear sensory-motor control slides]] <br>
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[[Media:2015_Non-linear_computational_lecture_compressed.pdf | Kathy's Non-linear sensory-motor control slides]] <br>
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[[Media:cosmo2015Bart.pdf | Bart's lecture slides - sensory-motor processing]] <br>
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[[Media:BartCodeCoSMo2015.zip | Bart's demo files]] <br>
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[[Media:matlabPyrToolsCoSMo2015Bart.zip | Pyr tools]] <br>
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[[Media:ReadingsCoSMo2015Bart1.zip | Bart's suggested further readings - part 1]] <br>
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[[Media:ReadingsCoSMo2015Bart2.zip | Bart's suggested further readings - part 2]] <br>
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 +
 +
'''Afternoon tutorial 1 - VOR (Jul 3)''' <br>
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[[Media:Cullen_Matlab_Exercise_and_Tutorial.zip | Tutorial material]] <br>
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 +
 +
'''Afternoon tutorial 2 - gain fields (Jul 4)''' <br>
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[[Media:gainModelCoSMo2015Bart.zip | Gain field tutorial]] <br>
 +
 +
----
 +
 +
 +
== Computational Methods in Neuroscience ==
 +
''Jul 6-7'' <br>
 +
Lecturers: Sophie Deneve, Robert van Beers <br>
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 +
[[Media:DeneveCoSMo2015.pdf | Sophie's slides - spike coding]] <br>
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[[Media:motor_adaptation_vanBeers_CoSMo2015.pdf | Rob van Beers slides - motor adaptation]] <br>
 +
 +
 +
'''Afternoon tutorial 1 - spike coding (Jul 6)''' <br>
 +
Implementation of spike coding in a single neuron and networks of neurons as described [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003258 here] (see also supplementary materials). <br>
 +
[[Media:Deneve_spike_coding_CoSMo2015.m | Here]] is some solution code. <br>
 +
 +
 +
'''Afternoon tutorial 2 - motor adaptation (Jul 7)''' <br>
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[[Media:exercises_motor_adaptationCoSMo2015_Rob.pdf | Tutorial instructions]] <br>
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[[Media:vanBeers_CoSMo2015_papers.zip | Papers related to the tutorial]] <br>
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[[Media:Answers_exercises_motor_adaptationCoSMo2015.zip | Exercise solutions]] <br>
 +
 +
----
 +
 +
 +
== Reach and grasp mechanisms ==
 +
''Jul 8-9'' <br>
 +
Lecturers: Hans Scherberger, Pieter Medendorp <br>
 +
 +
[[Media:Reaching_Medendorp_CoSMo2015.pdf | Pieter's slides - reaching]] <br>
 +
[[Media:Scherberger_slides_enc.pdf | Hans' slides - grasping]] <br>
 +
 +
 +
'''Tutorial 1 - reference frame transformations (morning)''' <br>
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[[Media:ReferenceFrameAnalysis)CoSMo2015Medendorp.pdf | Tutorial instructions]] <br>
 +
[[Media:reach_tutorial_files_CoSMo2015Medendorp.zip | Matlab code]] <br>
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[[Media:Reference_Frame_analysis_solutions_CoSMo2015.pdf | Explanation of solution]] <br>
 +
[[Media:Integ_Pieter_CoSMo2015.m | Solution Matlab code]] <br>
 +
 +
 +
'''Tutorial 2 - PRR single unit encoding/decoding (afternoon)''' <br>
 +
Data will be distributed on a memory stick (65Mb). <br>
 +
 +
----
 +
 +
 +
==Final Project Presentations - Jul 10, 3:00-6:30pm and 7:30-9:30pm==
 +
'''Instructions:''' Every group will have a 30min slot (15min presentation, 15min questions). The research question, hypotheses and rationale for the choice of the approach should be clearly presented. Models, simulations, results, discussion etc should be detailed enough for everyone to follow. <br>
 +
'''Best group gets a free poster OR short talk at TCMC 2015!!!''' (confirmed by John Krakauer) <br>
 +
 +
''3:00-3:30 - Saccadic ping-pong''<br>
 +
"Reward-based learning in saccadic adaptation tasks" '''WINNER !!!!!!!!!!''' <br>
 +
Group: Ondřej Havlíček, Svenja Gremmler, Hans-Christian Ruiz, Rebecca Sier, Mohsen Sadeghi <br>
 +
 +
''3:30-4:00 - The (Spanish) wave followers ''<br>
 +
"The effect of auditory nerve fibers loss on auditory steady-state responses elicited by sinusoidally amplitude modulated tones" <br>
 +
Group: Gerard Encina Llamas , Anna Metzger and Jose Garcia-Uceda <br>
 +
 +
''4:00-4:30 - Bayes'' <br>
 +
"Bayesian inference in the brain" <br>
 +
Group: Elahe Arani, Bahram Yoosefizonooz <br>
 +
 +
''4:30-5:00 - Life of Gamma'' <br>
 +
"Compensation Mechanisms in Predictive Neural Network Coding" <br>
 +
Group: Garret, Philippe, Yaz, Ahmed, David <br>
 +
 +
''5:00-5:30 - Not Magnetic'' <br>
 +
"Effect of external electric field on synaptic transmission" <br>
 +
Group: Alexander Kuck, Jing Chen, Leslie Guadron <br>
 +
 +
''5:30-6:00 - The Undecided'' <br>
 +
"Do we learn endpoints or trajectories in a point-to-point reaching task?" <br>
 +
Group: Hossein Rafipoor  and Evangelia-Regkina Symeonidou <br>
 +
 +
''6:00-6:30 - The Ball Catchers'' <br>
 +
"Me vs. the world: optimal integration of reference frames for interception" <br>
 +
Group: Yalda Mohsenzadeh, Antonella Pomante, Alessia Longo, Mathias Klinghammer, Florian Perdreau <br>
 +
 +
''Dinner'' <br>
 +
 +
''7:30-8:00 - The CoSMonkeys'' <br>
 +
"Predicting movement from the Neural code" <br>
 +
Group: Margaux, Pedro, Robin, Shlomi, Sigrid <br>
 +
 +
''8:00-8:30 - Synchronize With Resonance (SWR)'' <br>
 +
"Associating single cell properties with oscillations, resonance and communication" <br>
 +
Group: Sonal Sengupta, Chris Tatarau and Golan Karvat <br>
 +
 +
''8:30-9:00 - The No-Names'' <br>
 +
"How does degree of coherence of motion affect key press reaction time and accuracy about number of motion directions?" <br>
 +
Group: James Cooke, Tatyana Matveeva, Anna Geuzebroek, Roozbeh Farhoudi, Jason Fuller <br>
 +
 +
''9:00-9:30 - Laura Chaos on Eggs on a Keyser roll'' <br>
 +
"Modeling the effect of muscle vibration on proprioceptive estimation of hand location" <br>
 +
Group: Laura Mikula, Chao Gu, Johannes Keyser, EG Gaffin-Cahn <br>
 +
<br>
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 +
'''Vote for projects [https://www.surveymonkey.com/r/5S6BQ7K HERE] and [https://www.surveymonkey.com/r/5RQ8XLX HERE] (only for CoSMo attendants!)'''

Latest revision as of 14:46, 6 February 2018

This page contains course materials for the CoSMo 2015 summer school.

CoSMo logo

Introduction - overview of sensory-motor control

Jun 29-30
Lecturers: Gunnar Blohm, Paul Schrater, Konrad Kording, John van Opstal, Pieter Medendorp

Konrad, Weiji, Dan book book

Blohm slides part 1 - computational anatomy
Schrater slides part 1 - decision making

Schrater slides part 2 - sensory-motor systems
Blohm slides part 2 - sensory-motor processing underlying eye movements
van Opstal syllabus - linear systems theory and answers to exercises part 1 and part 2
van Opstal slides 1 - linear systems theory
van Opstal slides 2 - linear systems in sensory-motor control A
van Opstal slides 3 - linear systems in sensory-motor control B
van Opstal slides 4 - Laplace transformation
van Opstal slides 5 - The saccadic system


Afternoon tutorial 1 - Bayesian decoding (Jun 29)
Bayesian decoding tutorial and related Data set


Afternoon tutorial 2 - Saccades (Jun 30)
Saccade models (Simulink code)
Example of additional ways to implement a saccade model using Matlab linear systems toolbox or direct integration of the differential equations underlying the linear systems approach: Simple saccade model


How to model tutorial

Jun 29 (evening)
Lecturers: Gunnar Blohm, Paul Schrater, Konrad Kording

tutorial slides


DREAM database - Shared data and models for CoSMo projects

Jun 29 - Jul 10

Curtesy: Konrad Kording

You can get the DREAM project from Gunnar on a USB drive. DREAM can also be downloaded piece-wise (data sets, models, tools, and documentation) from CRCNS: http://crcns.org/data-sets/movements/dream/downloading-dream. You will need to create an account on CRCNS to be able to download the project files. If you want "all" of DREAM (models, tools, and documentation), click here: AllDream.zip

If you're familiar with svn and would like info/credentials for code in the repository, contact Ben Walker


Here's the latest version of LoadDreamPaths.m. (This script should work for all OSes.)


Here is a description of data sets currently in Dream. Dream is growing, but this list is accurate as of the time of the summer school (click on the link to access the related publication).

  • Burns -- reaching with head tilt and left/right visual perturbations
  • Corbett -- reach trajectory predictions based on EMG and gaze movements
  • Fernandes -- reaching with uncertain and rotated midpoint feedback
  • Flint -- decoding of reaching movements from local field potentials
  • Kording -- reaching with uncertain midpoint feedback
  • Mattar 07 -- generalizing from one, two or multi targets to another direction
  • Mattar 10 -- reaching to a distance (short/long), generalizing to the other one (long/short)
  • Ostry -- move in force field, get an estimation of where the hand is
  • Scott -- monkey (no spike), center out: even and not evenly distributed targets, also a forward/back
  • Stevenson -- center out, monkey with neural time stamps
  • Thoroughman -- reach adaptation to perturbations with different complexity
  • Vahdat -- movement in force field with FMRI scans pre/post learning
  • Wei 08 -- visual perturbations, cursor shown only at target
  • Wei 10 -- movement in differing force fields
  • Young -- movement time stayed the same, but distance changed; fast, medium, slow reaches.


How to write papers

Jun 30 (evening)
Lecturer: Konrad Kording

Paper structuring paper


Coding & decoding

Jul 1
Lecturers: Joern Diedrichsen, Nikolaus Kriegeskorte

Please read the following papers BEFORE the tutorial: Ejaz, et al., 2015 and Khaligh-Razavi & Kriegeskorte, 2014

Niko's slides
Joern's slides - Part 1
Joern's slides - Part 2

If you would like to apply these methods, please refer to this paper. The link to the Matlab code can be found within the paper. Accompanying tutorial videos can be found here.


Motor learning & control

Jul 2
Lecturers: Stefan Glasauer, John van Opstal

Stefan's lectures
Accompanying code


Multisensory processing

Jul 3-4
Lecturers: Kathy Cullen, Bart Krekelberg

Kathy's linear sensory-motor control slides
Kathy's Non-linear sensory-motor control slides

Bart's lecture slides - sensory-motor processing
Bart's demo files
Pyr tools
Bart's suggested further readings - part 1
Bart's suggested further readings - part 2


Afternoon tutorial 1 - VOR (Jul 3)
Tutorial material


Afternoon tutorial 2 - gain fields (Jul 4)
Gain field tutorial


Computational Methods in Neuroscience

Jul 6-7
Lecturers: Sophie Deneve, Robert van Beers

Sophie's slides - spike coding
Rob van Beers slides - motor adaptation


Afternoon tutorial 1 - spike coding (Jul 6)
Implementation of spike coding in a single neuron and networks of neurons as described here (see also supplementary materials).
Here is some solution code.


Afternoon tutorial 2 - motor adaptation (Jul 7)
Tutorial instructions
Papers related to the tutorial
Exercise solutions


Reach and grasp mechanisms

Jul 8-9
Lecturers: Hans Scherberger, Pieter Medendorp

Pieter's slides - reaching
Hans' slides - grasping


Tutorial 1 - reference frame transformations (morning)
Tutorial instructions
Matlab code
Explanation of solution
Solution Matlab code


Tutorial 2 - PRR single unit encoding/decoding (afternoon)
Data will be distributed on a memory stick (65Mb).


Final Project Presentations - Jul 10, 3:00-6:30pm and 7:30-9:30pm

Instructions: Every group will have a 30min slot (15min presentation, 15min questions). The research question, hypotheses and rationale for the choice of the approach should be clearly presented. Models, simulations, results, discussion etc should be detailed enough for everyone to follow.
Best group gets a free poster OR short talk at TCMC 2015!!! (confirmed by John Krakauer)

3:00-3:30 - Saccadic ping-pong
"Reward-based learning in saccadic adaptation tasks" WINNER !!!!!!!!!!
Group: Ondřej Havlíček, Svenja Gremmler, Hans-Christian Ruiz, Rebecca Sier, Mohsen Sadeghi

3:30-4:00 - The (Spanish) wave followers
"The effect of auditory nerve fibers loss on auditory steady-state responses elicited by sinusoidally amplitude modulated tones"
Group: Gerard Encina Llamas , Anna Metzger and Jose Garcia-Uceda

4:00-4:30 - Bayes
"Bayesian inference in the brain"
Group: Elahe Arani, Bahram Yoosefizonooz

4:30-5:00 - Life of Gamma
"Compensation Mechanisms in Predictive Neural Network Coding"
Group: Garret, Philippe, Yaz, Ahmed, David

5:00-5:30 - Not Magnetic
"Effect of external electric field on synaptic transmission"
Group: Alexander Kuck, Jing Chen, Leslie Guadron

5:30-6:00 - The Undecided
"Do we learn endpoints or trajectories in a point-to-point reaching task?"
Group: Hossein Rafipoor and Evangelia-Regkina Symeonidou

6:00-6:30 - The Ball Catchers
"Me vs. the world: optimal integration of reference frames for interception"
Group: Yalda Mohsenzadeh, Antonella Pomante, Alessia Longo, Mathias Klinghammer, Florian Perdreau

Dinner

7:30-8:00 - The CoSMonkeys
"Predicting movement from the Neural code"
Group: Margaux, Pedro, Robin, Shlomi, Sigrid

8:00-8:30 - Synchronize With Resonance (SWR)
"Associating single cell properties with oscillations, resonance and communication"
Group: Sonal Sengupta, Chris Tatarau and Golan Karvat

8:30-9:00 - The No-Names
"How does degree of coherence of motion affect key press reaction time and accuracy about number of motion directions?"
Group: James Cooke, Tatyana Matveeva, Anna Geuzebroek, Roozbeh Farhoudi, Jason Fuller

9:00-9:30 - Laura Chaos on Eggs on a Keyser roll
"Modeling the effect of muscle vibration on proprioceptive estimation of hand location"
Group: Laura Mikula, Chao Gu, Johannes Keyser, EG Gaffin-Cahn

Vote for projects HERE and HERE (only for CoSMo attendants!)

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